The Earth's population is facing global warming and one of the dramatic repercussions of this phenomenon is the decrease in the supply of drinking water. Against the acute background of diminishing water resources, a new cause for concern has arisen, namely the pollution of drinking water sources with various types of contaminants. The present chapter aims to briefly address the issue of microbiome study in aquatic ecosystems by conducting a literature review realized through searching for articles related to this topic, published in the PubMed database between 2011 and 2024. The objective is to quantify the extent of the scientific world's concern towards this phenomenon in an indirect way, namely by analyzing the reporting of results. The study establishes the pandemic period as a reference, thus realizing a temporal distribution of the studies identified in the literature. The decision to choose the pandemic period as a benchmark was due by the objective reason of the increase in antibiotic consumption due to the existence of a large number of Covid-19 cases of illness. Even before the period mentioned there were also concerns about this issue. Today, the reasons for concern have become increasingly evident in view of the growing resistance to antibiotics.